This paper established a simulation model to integrate surface water and groundwater resources allocation of southern Taiwan. Based on forecasted future demand and supply system of water resources on the year 2011, three strategies to allocate water resources were tested under different hydrological conditions and constraints on groundwater pumpage. Two major conclusions were made according to simulation results: (1) If groundwater pumpage is constrainted on current level, for the strategy of maximizing benefits of water use, irrigation demands will have shortage and for the priorities of water use purposes, industrial water demands will be not satisfied. Besides, for the strategy based on the priority of water rights, aquaculture water supplies can not be satisfied. (2) If groundwater pumpage is constrainted on yearly quantity of recharge, considering above three strategies to allocate water resources, all demands of water use purposes will have shortage.